Bacterial Metalloenzymes Research Articles

Inhibitors of Selected Bacterial Metalloenzymes.

The utilization of bacterial metalloenzymes, especially ones not having mammalian (human) counterparts, has drawn attention to develop novel antibacterial agents to overcome drug resistance and especially multidrug resistance. In this review, we focus on the recent achievements on the development of inhibitors of bacterial enzymes peptide deformylase (PDF), metallo-β-lactamase (MBL), methionine aminopeptidase (MetAP) and UDP-3-O-acyl- N-acetylglucosamine deacetylase (LpxC). The state of the art of the design and investigation of inhibitors of bacterial metalloenzymes is presented, and challenges are outlined and discussed.

Gut Microbiota: Rational Manipulation of Gut Bacterial Metalloenzymes Provides Insights into Dysbiosis and Inflammation.

ADVERTISEMENT RETURN TO ISSUEPREVViewpointNEXTGut Microbiota: Rational Manipulation of Gut Bacterial Metalloenzymes Provides Insights into Dysbiosis and InflammationVayu M. RekdalVayu M. RekdalDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United StatesMore by Vayu M. Rekdal and Emily P. Balskus*Emily P. BalskusDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States*E-mail: [email protected]More by Emily P. Balskushttp://orcid.org/0000-0001-5985-5714Cite this: Biochemistry 2018, 57, 16, 2291–2293Publication Date (Web):April 10, 2018Publication History Received21 March 2018Published online10 April 2018Published inissue 24 April 2018https://doi.org/10.1021/acs.biochem.8b00340Copyright © 2018 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2581Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (609 KB) Get e-AlertsSUBJECTS:Anions,Bacteria,Inflammation,Molybdenum,Peptides and proteins Get e-Alerts

The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes

An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.

Adiabaticity of the proton-coupled electron-transfer step in the reduction of superoxide effected by nickel-containing superoxide dismutase metallopeptide-based mimics.

Nickel-containing superoxide dismutases (NiSODs) are bacterial metalloenzymes that catalyze the disproportionation of O2(-). These enzymes take advantage of a redox-active nickel cofactor, which cycles between the Ni(II) and Ni(III) oxidation states, to catalytically disprotorptionate O2(-). The Ni(II) center is ligated in a square planar N2S2 coordination environment, which, upon oxidation to Ni(III), becomes five-coordinate following the ligation of an axial imidazole ligand. Previous studies have suggested that metallopeptide-based mimics of NiSOD reduce O2(-) through a proton-coupled electron transfer (PCET) reaction with the electron derived from a reduced Ni(II) center and the proton from a protonated, coordinated Ni(II)-S(H(+))-Cys moiety. The current work focuses on the O2(-) reduction half-reaction of the catalytic cycle. In this study we calculate the vibronic coupling between the reactant and product diabatic surfaces using a semiclassical formalism to determine if the PCET reaction is proceeding through an adiabatic or nonadiabatic proton tunneling process. These results were then used to calculate H/D kinetic isotope effects for the PCET process. We find that as the axial imidazole ligand becomes more strongly associated with the Ni(II) center during the PCET reaction, the reaction becomes more nonadiabatic. This is reflected in the calculated H/D KIEs, which moderately increase as the reaction becomes more nonadiabatic. Furthermore, the results suggest that as the axial ligand becomes less Lewis basic the observed reaction rate constants for O2(-) reduction should become faster because the reaction becomes more adiabatic. These conclusions are in-line with experimental observations. The results thus indicate that variations in the axial donor's ability to coordinate to the nickel center of NiSOD metallopeptide-based mimics will strongly influence the fundamental nature of the O2(-) reduction process.

Steric Control of the Hi‐CO MoFe Nitrogenase Complex Revealed by Stopped‐Flow Infrared Spectroscopy

Here, we report the impact of substitution for the α-70Val residue of Azotobacter vinelandii nitrogenase molybdenum-iron (MoFe) protein on the so-called “hi-CO” CO bound complex as monitored in real-time by stopped-flow infra-red (SF-IR) spectroscopy. Nitrogenase is a bacterial metalloenzyme system whose physiological function is to catalyze the reduction of dinitrogen to ammonia [1, 2] with a concomitant reduction of 2H+ to H2 and hydrolysis of MgATP. X-ray crystallography on MoFe nitrogenase reveals the active-site FeMo-cofactor to be an unprecedented [Fe7S9MoX:homocitrate] cluster [3, 4], figure 1. However, simple inspection of this structure does not provide an obvious location for substrate binding or any indication of the subsequent mechanism for substrate reduction. Mechanisms focused on substrate binding to either Mo and Fe sites have been proposed as have combination approaches that involve migration of substrate-derived moieties between metal atoms during reduction [5–8].

Efficacy of Calcium-EDTA as an Inhibitor for Metallo-β-Lactamase in a Mouse Model of Pseudomonas aeruginosa Pneumonia

In this study, we have evaluated the efficacy of calcium-EDTA (Ca-EDTA) as an inhibitor of bacterial metalloenzymes, such as metallo-β-lactamase (MBL) and other proteases, in a mouse model of Pseudomonas aeruginosa pneumonia. The simultaneous presence of Ca-EDTA (32 μg/ml) reduced the MICs of imipenem (IPM) in all MBL-producing P. aeruginosa isolates (IMP-1, -2, -7, and -10 and VIM-2) but not non-MBL-producing strains. In the pneumonia model, mice were intranasally infected with MBL-producing P. aeruginosa and then kept under conditions of hyperoxia to mimic ventilator-associated pneumonia. With both intranasal and subcutaneous administrations, Ca-EDTA significantly potentiated survival benefits of IPM compared to those of IPM alone. Ca-EDTA combination therapy induced a significant reduction of the bacterial burden in the lungs (P < 0.05). Furthermore, the inhibition activity of Ca-EDTA against MBL activity was confirmed by using the purified IMP-1 enzyme, which was characterized by a 50% inhibitory concentration (IC(50)) of 55 ± 8.2 μM. Finally, the protective effects of Ca-EDTA were demonstrated by culture supernatant-induced epithelial cell damage and acute lung injury in mice. These data suggest the therapeutic potential of Ca-EDTA not only by the blocking of MBLs but also by neutralizing tissue-damaging metalloproteases in P. aeruginosa infections.

Targeting the Peptide Deformylase of Mycobacterium tuberculosis Leads to Drug Discovery

Abstract: Peptide deformylase (PDF) is a ubiquitous bacterial metalloenzyme responsible to cleave the formyl group from nascent polypeptides, supporting in the maturation. It plays a vital role in the survival of bacterial cells which is con-served in the eubacteria and is considered to be an attractive target for developing new antibacterial agents. Homology modeling was employed for generation of 3-D structure of PDF of M. tuberculosis H37Rv and showed 92.5% amino acid in the allowed region of Ramachandran plot. PDF was used as target for a set of inhibitors with substantial structural dif-ferences. Docking results show that the BB-3497, BBS-54, Actinonin and BBS-02 bind with high affinity to enzyme ac-tive site. Phylogeny of PDF in M. tuberculosis H37Rv shows homology with other strains of pathogenic bacteria. These data validate PDF as a novel target for the design of a new generation of antimycobacterial agents. Keywords: Mycobacterium tuberculosis, Peptide deformylase, Docking, Phylogeny, Drugs.

Targeting Bacterial Metalloenzymes: A New Strategy for the Development of Anti-Infective Agents

Targeting Bacterial Metalloenzymes: A New Strategy for the Development of Anti-Infective Agents

Probing Variable Axial Ligation in Nickel Superoxide Dismutase Utilizing Metallopeptide-Based Models: Insight into the Superoxide Disproportionation Mechanism

Nickel superoxide dismutase (NiSOD) is a bacterial metalloenzyme that possesses a mononuclear Ni-center and catalyzes the disproportionation of O2*- by cycling between NiII and NiIII oxidation states. Herein we present evidence from several SOD active metallopeptide maquettes ([Ni(SODM2H(1)X)]; SODM2H(1)X = H2N-XCDLPCG-COOH; X = H, D, or A) that the Ni-center of NiSOD most likely remains five-coordinate during SOD catalysis using thin-film voltammetry. N3- and CN- titration studies suggest that O2*- disproportionation by [Ni(SODM2H(1)X)] proceeds via an outersphere mechanism. Computationally derived values for the nuclear reorganization energy of the [NiII(SODM2)]/[NiIII(SODM2)] self-exchange reaction combined with the experimentally determined value for ko ( approximately 450 s-1) suggest that axial ligation enhances the O2*- disproportionation reaction in [Ni(SODM2)] (and NiSOD by analogy) by optimizing the NiII/NiIII redox couple such that it is close to the midpoint of the O2*- reduction and oxidation couples.

Mechanism of Time-Dependent Inhibition of Polypeptide Deformylase by Actinonin

Polypeptide deformylase (PDF) is an essential bacterial metalloenzyme responsible for the removal of the N-formyl group from the N-terminal methionine of nascent polypeptides. Inhibition of bacterial PDF enzymes by actinonin, a naturally occurring antibacterial agent, has been characterized using steady-state and transient kinetic methods. Slow binding of actinonin to these enzymes is observed under steady-state conditions. Progress curve analysis is consistent with a two-step binding mechanism, in which tightening of the initial encounter complex (EI) results in a final complex (EI*) with an extremely slow, but observable, off-rate (t(1/2) for inhibitor dissociation >or=0.77 days). Stopped-flow measurement of PDF fluorescence confirms formation of EI and provides a direct measurement of the association rate. Rapid dilution studies establish that the potency of actinonin is enhanced by more than 2000-fold upon tightening of EI to form EI*, from K(i) = 530 nM (EI) to Ki*<or= 0.23 nM (EI*). In sharp contrast, the previously reported small molecule PDF inhibitor, SB-543668, is a competitive, readily reversible inhibitor (t(1/2) for dissociation = 2.8 s). In addition, we demonstrate that BB-3497 is also a time-dependent inhibitor of PDF with an extremely slow off-rate. The two-step inhibition model detailed herein for the inhibition of Staphylococcus aureus PDF by actinonin and BB-3497 is consistent with a recent report on the time-dependent inhibition of Escherichia coli PDF by a macrocyclic peptidomimetic inhibitor [Ngugen, K. T., et al. (2004) Bioorg. Chem. 32, 178-191]. This study substantially extends our understanding of PDF inhibition and may facilitate the development of novel antibiotics.

Targeting metalloenzymes: a strategy that works.

Faced with a wealth of antibacterial drug discovery targets as a result of bacterial genomics, we need to carefully select which ones to work with. Choosing bacterial metalloenzymes is one possible approach that can increase the probability of success. Metalloenzymes can be identified through specific motif searches of bacterial genomes. Current state-of-the-art medicinal chemistry allows for the design of inhibitor libraries targeting metalloenzymes and the efficient optimization of leads identified. This approach has been successfully applied to the discovery of in vivo active antibacterial agents that are inhibitors of bacterial peptide deformylase and UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase. Other bacterial metalloenzymes are open to the same approach.

Peptide Deformylase Inhibitors, Potential for a New Class of Broad Spectrum Antibacterials

Peptide deformylase (PDF) has emerged as one of the most promising new targets for antimicrobial chemotherapy. PDF is an essential bacterial metalloenzyme that deformylates the N-formylmethionine of newly synthesised bacterial polypeptides. Although the enzyme has been known for over 30 years, it has proved difficult to isolate and characterise due to its apparent instability. However, recent progress in understanding the structure and function of PDF has greatly facilitated the drug discovery process. In this article we review the potential of PDF as an antibacterial target and highlight progress in the development of inhibitors of PDF. The field has evolved particularly rapidly through the use of high throughput screening and combinatorial techniques and the diverse series of structures exploited previously in other metalloenzyme programmes. Although many different structural classes of compounds have been reported as inhibitors of PDF, the real challenge has been in obtaining molecules with good a ntibacterial activity. Several PDF inhibitors have now been described that demonstrate potent in vitro antibacterial activity against a range of Gram-negative and Gram-positive drug resistant pathogens. Results in stringent animal models of infection suggest that for some of these molecules good in vitro activity translates into good in vivo efficacy. One of the most encouraging compounds reported, BB-83698, has shown activity against Streptococcus pneumoniae in both the neutropenic mouse thigh and lung infection models. These data suggest that PDF inhibitors are a promising new class of antibacterial agents with opportunities to treat respiratory and other bacterial infections. Keywords: peptide deformylase, broad spectrum antibacterial, bacterial polypeptode, bb-83698, pdf inhibitor

What is the ultimate fate of superoxide anion in vivo?

For three decades, oxidative stress and the role of reactive oxygen species in biology have been extensively studied. Recently, a new interest in these areas has emerged with the discovery of superoxide reductases, a family of familiar bacterial metalloenzymes whose heretofore unknown function has now been apparently revealed. In a series of experiments utilizing genetic, molecular biological, and biochemical methods, these enzymes have been shown to be physiologically competent at removing superoxide. The role of these enzymes and their biological relationship to the well-known superoxide dismutases is discussed.

Antibiotic Activity and Characterization of BB-3497, a Novel Peptide Deformylase Inhibitor

Peptide deformylase (PDF) is an essential bacterial metalloenzyme which deformylates the N-formylmethionine of newly synthesized polypeptides and as such represents a novel target for antibacterial chemotherapy. To identify novel PDF inhibitors, we screened a metalloenzyme inhibitor library and identified an N-formyl-hydroxylamine derivative, BB-3497, and a related natural hydroxamic acid antibiotic, actinonin, as potent and selective inhibitors of PDF. To elucidate the interactions that contribute to the binding affinity of these inhibitors, we determined the crystal structures of BB-3497 and actinonin bound to Escherichia coli PDF at resolutions of 2.1 and 1.75 A, respectively. In both complexes, the active-site metal atom was pentacoordinated by the side chains of Cys 90, His 132, and His 136 and the two oxygen atoms of N-formyl-hydroxylamine or hydroxamate. BB-3497 had activity against gram-positive bacteria, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis, and activity against some gram-negative bacteria. Time-kill analysis showed that the mode of action of BB-3497 was primarily bacteriostatic. The mechanism of resistance was via mutations within the formyltransferase gene, as previously described for actinonin. While actinonin and its derivatives have not been used clinically because of their poor pharmacokinetic properties, BB-3497 was shown to be orally bioavailable. A single oral dose of BB-3497 given 1 h after intraperitoneal injection of S. aureus Smith or methicillin-resistant S. aureus protected mice from infection with median effective doses of 8 and 14 mg/kg of body weight, respectively. These data validate PDF as a novel target for the design of a new generation of antibacterial agents.

The interaction of some microbial and mammalian proteinases with human blood trypsin inhibitors

It has been shown that trypsin inhibitors in human serum inhibit the microbial serine proteinases subtilisin, aspergillopeptidase B, and the enzymes from Streptomyces griseus. The inhibition of these enzymes by serum was compared with the inhibition of the homologous mammalian proteinases trypsin, chymotrypsin, and elastase. The microbial proteinases were found to interact with larger quantities of the inhibitors in serum and are, therefore, less effectively inhibited by serum than the mammalian enzymes. In addition to serine proteinases, the bacterial metalloenzyme thermolysin also interacts with the inhibitors but is not appreciably inhibited by them. It was shown that the enzyme molecules must have intact active sites for the enzyme-inhibitor reaction to occur. It is suggested that the function of trypsin inhibitors is to protect tissues against the action of serine proteinases of both endogenous and exogenous origin.